ok if a site has over 10,000 inlinks/backlinks what would be the problem then if the site is not ranking at all?

The site was ranking then dropped then came back and now dropped and still that way for some time now. Yahoo's index is only showing about 50 out 700 pages of the site. Not sure why it's not indexing more then that but hope someone could shed some light on this.

Is there a possibility that Yahoo is penalizing with URLs looking like this